How was it that the SPARTAN-II in the Halo Graphic Novel story "Armor Testing" was able to retire?

Answer:

That's classified. Put it this way, she didn't simply up and say "Oh, I'm off to have a baby, peace out."

With all sympathy towards the desire for children, it's good to know that the criteria allowing elite super soldiers to retire in the face of the extermination of the species are at least -how shall we say?- rigourous.

(Unless her being allowed to leave and have a child was in itself an ONI experiment, with or without her knowledge, to test the alterations passed on...)